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Work 1-10 of 61

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Article

Estimation of dynamic flux profiles from metabolic time series data

by Eberhard Voit; I-Chun Chou

2012

Subjects
  • Engineering, Biomedical
  • File Download
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Background: Advances in modern high-throughput techniques of molecular biology have enabled top-down approaches for the estimation of parameter values in metabolic systems, based on time series data. Special among them is the recent method of dynamic flux estimation (DFE), which uses such data not only for parameter estimation but also for the identification of functional forms of the processes governing a metabolic system. DFE furthermore provides diagnostic tools for the evaluation of model validity and of the quality of a model fit beyond residual errors. Unfortunately, DFE works only when the data are more or less complete and the system contains as many independent fluxes as metabolites. These drawbacks may be ameliorated with other types of estimation and information. However, such supplementations incur their own limitations. In particular, assumptions must be made regarding the functional forms of some processes and detailed kinetic information must be available, in addition to the time series data.Results: The authors propose here a systematic approach that supplements DFE and overcomes some of its shortcomings. Like DFE, the approach is model-free and requires only minimal assumptions. If sufficient time series data are available, the approach allows the determination of a subset of fluxes that enables the subsequent applicability of DFE to the rest of the flux system. The authors demonstrate the procedure with three artificial pathway systems exhibiting distinct characteristics and with actual data of the trehalose pathway in Saccharomyces cerevisiae.Conclusions: The results demonstrate that the proposed method successfully complements DFE under various situations and without a priori assumptions regarding the model representation. The proposed method also permits an examination of whether at all, to what degree, or within what range the available time series data can be validly represented in a particular functional format of a flux within a pathway system. Based on these results, further experiments may be designed to generate data points that genuinely add new information to the structure identification and parameter estimation tasks at hand. © 2012 Chou and Voit; licensee BioMed Central Ltd.

Article

Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket

by Pierrick Craveur; Anna T. Gres; Karen Kirby; Dandan Liu; John A. Hammond; Yisong Deng; Stefano Forli; David S. Goodsell; James R. Williamson; Stefan Sarafianos; Arthur J. Olson

2019

Subjects
  • Health Sciences, Public Health
  • Biology, Microbiology
  • Biology, Molecular
  • File Download
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HIV-1 capsid protein (CA) plays critical roles in both early and late stages of the viral replication cycle. Mutagenesis and structural experiments have revealed that capsid core stability significantly affects uncoating and initiation of reverse transcription in host cells. This has led to efforts in developing antivirals targeting CA and its assembly, although none of the currently identified compounds are used in the clinic for treatment of HIV infection. A specific interaction that is primarily present in pentameric interfaces in the HIV-1 capsid core was identified and is reported to be important for CA assembly. This is shown by multidisciplinary characterization of CA site-directed mutants using biochemical analysis of virus-like particle formation, transmission electron microscopy of in vitro assembly, crystallographic studies, and molecular dynamic simulations. The data are consistent with a model where a hydrogen bond between CA residues E28 and K30= from neighboring N-terminal domains (CA NTD s) is important for CA pentamer interactions during core assembly. This pentamer-preferred interaction forms part of an N-terminal domain interface (NDI) pocket that is amenable to antiviral targeting.

Article

A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein

by Anurag Sethi; Jianhui Tian; Cynthia Derdeyn; Bette Korber; S. Gnanakaran

2013

Subjects
  • Biology, Microbiology
  • Health Sciences, Public Health
  • File Download
  • View Abstract

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The HIV-1 envelope (Env) spike, which consists of a compact, heterodimeric trimer of the glycoproteins gp120 and gp41, is the target of neutralizing antibodies. However, the high mutation rate of HIV-1 and plasticity of Env facilitates viral evasion from neutralizing antibodies through various mechanisms. Mutations that are distant from the antibody binding site can lead to escape, probably by changing the conformation or dynamics of Env; however, these changes are difficult to identify and define mechanistically. Here we describe a network analysis-based approach to identify potential allosteric immune evasion mechanisms using three known HIV-1 Env gp120 protein structures from two different clades, B and C. First, correlation and principal component analyses of molecular dynamics (MD) simulations identified a high degree of long-distance coupled motions that exist between functionally distant regions within the intrinsic dynamics of the gp120 core, supporting the presence of long-distance communication in the protein. Then, by integrating MD simulations with network theory, we identified the optimal and suboptimal communication pathways and modules within the gp120 core. The results unveil both strain-dependent and -independent characteristics of the communication pathways in gp120. We show that within the context of three structurally homologous gp120 cores, the optimal pathway for communication is sequence sensitive, i.e. a suboptimal pathway in one strain becomes the optimal pathway in another strain. Yet the identification of conserved elements within these communication pathways, termed inter-modular hotspots, could present a new opportunity for immunogen design, as this could be an additional mechanism that HIV-1 uses to shield vulnerable antibody targets in Env that induce neutralizing antibody breadth.

Article

Assessing the Hemodynamic Impact of Anterior Leaflet Laceration in Transcatheter Mitral Valve Replacement: An in silico Study

by Keshav Kohli; Zhenglun A Wei; Vahid Sadri; Andrew W Siefert; Philipp Blanke; Emily Perdoncin; Adam Greenbaum; Jaffar M Khan; Robert Lederman; Vasilis Babaliaros; Ajit Yoganathan; John Oshinski

2022

Subjects
  • Health Sciences, Radiology
  • Engineering, Biomedical
  • File Download
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Background: A clinical study comparing the hemodynamic outcomes of transcatheter mitral valve replacement (TMVR) with vs. without Laceration of the Anterior Mitral leaflet to Prevent Outflow Obstruction (LAMPOON) has never been designed nor conducted. Aims: To quantify the hemodynamic impact of LAMPOON in TMVR using patient-specific computational (in silico) models. Materials: Eight subjects from the LAMPOON investigational device exemption trial were included who had acceptable computed tomography (CT) data for analysis. All subjects were anticipated to be at prohibitive risk of left ventricular outflow tract (LVOT) obstruction from TMVR, and underwent successful LAMPOON immediately followed by TMVR. Using post-procedure CT scans, two 3D anatomical models were created for each subject: (1) TMVR with LAMPOON (performed procedure), and (2) TMVR without LAMPOON (virtual control). A validated computational fluid dynamics (CFD) paradigm was then used to simulate the hemodynamic outcomes for each condition. Results: LAMPOON exposed on average 2 ± 0.6 transcatheter valve cells (70 ± 20 mm2 total increase in outflow area) which provided an additional pathway for flow into the LVOT. As compared to TMVR without LAMPOON, TMVR with LAMPOON resulted in lower peak LVOT velocity, lower peak LVOT gradient, and higher peak LVOT effective orifice area by 0.4 ± 0.3 m/s (14 ± 7% improvement, p = 0.006), 7.6 ± 10.9 mmHg (31 ± 17% improvement, p = 0.01), and 0.2 ± 0.1 cm2 (17 ± 9% improvement, p = 0.002), respectively. Conclusion: This was the first study to permit a quantitative, patient-specific comparison of LVOT hemodynamics following TMVR with and without LAMPOON. The LAMPOON procedure achieved a critical increment in outflow area which was effective for improving LVOT hemodynamics, particularly for subjects with a small neo-left ventricular outflow tract (neo-LVOT).

Article

Hydrodynamic modulation of pluripotent stem cells

by Krista M Fridley; Melissa A Kinney; Todd McDevitt

2012

Subjects
  • Engineering, Biomedical
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Controlled expansion and differentiation of pluripotent stem cells (PSCs) using reproducible, high-throughput methods could accelerate stem cell research for clinical therapies. Hydrodynamic culture systems for PSCs are increasingly being used for high-throughput studies and scale-up purposes; however, hydrodynamic cultures expose PSCs to complex physical and chemical environments that include spatially and temporally modulated fluid shear stresses and heterogeneous mass transport. Furthermore, the effects of fluid flow on PSCs cannot easily be attributed to any single environmental parameter since the cellular processes regulating self-renewal and differentiation are interconnected and the complex physical and chemical parameters associated with fluid flow are thus difficult to independently isolate. Regardless of the challenges posed by characterizing fluid dynamic properties, hydrodynamic culture systems offer several advantages over traditional static culture, including increased mass transfer and reduced cell handling. This article discusses the challenges and opportunities of hydrodynamic culture environments for the expansion and differentiation of PSCs in microfluidic systems and larger-volume suspension bioreactors. Ultimately, an improved understanding of the effects of hydrodynamics on the self-renewal and differentiation of PSCs could yield improved bioprocessing technologies to attain scalable PSC culture strategies that will probably be requisite for the development of therapeutic and diagnostic applications.

Article

Fully-coupled fluid-structure interaction simulation of the aortic and mitral valves in a realistic 3D left ventricle model

by Wenbin Mao; Andres Caballero; Raymond Mckay; Charles Primiano; Wei Sun

2017

Subjects
  • Engineering, Biomedical
  • Physics, Elementary Particles and High Energy
  • Computer Science
  • Biology, Biostatistics
  • File Download
  • View Abstract

Abstract:Close

In this study, we present a fully-coupled fluid-structure interaction (FSI) framework that combines smoothed particle hydrodynamics (SPH) and nonlinear finite element (FE) method to investigate the coupled aortic and mitral valves structural response and the bulk intraventricular hemodynamics in a realistic left ventricle (LV) model during the entire cardiac cycle. The FSI model incorporates valve structures that consider native asymmetric leaflet geometries, anisotropic hyperelastic material models and human material properties. Comparison of FSI results with subject-specific echocardiography data demonstrates that the SPH-FE approach is able to quantitatively predict the opening and closing times of the valves, the mitral leaflet opening and closing angles, and the large-scale intraventricular flow phenomena with a reasonable agreement. Moreover, comparison of FSI results with a LV model without valves reveals substantial differences in the flow field. Peak systolic velocities obtained from the FSI model and the LV model without valves are 2.56 m/s and 1.16 m/s, respectively, compared to the Doppler echo data of 2.17 m/s. The proposed SPH-FE FSI framework represents a further step towards modeling patient-specific coupled LV-valve dynamics, and has the potential to improve our understanding of cardiovascular physiology and to support professionals in clinical decision-making.

Article

Modeling the generation of output by the cerebellar nuclei

by Volker Steuber; Dieter Jaeger

2013

Subjects
  • Biology, Neuroscience
  • Computer Science
  • File Download
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Abstract:Close

Functional aspects of network integration in the cerebellar cortex have been studied experimentally and modeled in much detail ever since the early work by theoreticians such as Marr, Albus and Braitenberg more than 40years ago. In contrast, much less is known about cerebellar processing at the output stage, namely in the cerebellar nuclei (CN). Here, input from Purkinje cells converges to control CN neuron spiking via GABAergic inhibition, before the output from the CN reaches cerebellar targets such as the brainstem and the motor thalamus. In this article we review modeling studies that address how the CN may integrate cerebellar cortical inputs, and what kind of signals may be transmitted. Specific hypotheses in the literature contrast rate coding and temporal coding of information in the spiking output from the CN. One popular hypothesis states that post-inhibitory rebound spiking may be an important mechanism by which Purkinje cell inhibition is turned into CN output spiking, but this hypothesis remains controversial. Rate coding clearly does take place, but in what way it may be augmented by temporal codes remains to be more clearly established. Several candidate mechanisms distinct from rebound spiking are discussed, such as the significance of spike time correlations between Purkinje cell pools to determine CN spike timing, irregularity of Purkinje cell spiking as a determinant of CN firing rate, and shared brief pauses between Purkinje cell pools that may trigger individual CN spikes precisely.

Article

Diffusion-weighted MRI with intravoxel incoherent motion modeling for assessment of muscle perfusion in the thigh during post-exercise hyperemia in younger and older adults

by Fatemeh Adelnia; Michelle Shardell; Christopher M. Bergeron; Kenneth W. Fishbein; Richard G. Spencer; Luigi Ferrucci; David Reiter

2019

Subjects
  • Biophysics, Medical
  • Health Sciences, Radiology
  • Health Sciences, Human Development
  • Gerontology
  • File Download
  • View Abstract

Abstract:Close

Aging is associated with impaired endothelium-dependent vasodilation that leads to muscle perfusion impairment and contributes to organ dysfunction. Impaired muscle perfusion may result in inadequate delivery of oxygen and nutrients during and after muscle contraction, leading to muscle damage. The ability to study the relationship between perfusion and muscle damage has been limited using traditional muscle perfusion measures, which are invasive and risky. To overcome this limitation, we optimized a diffusion-weighted MRI sequence and validated an intravoxel incoherent motion (IVIM) analysis based on Monte Carlo simulation to study muscle perfusion impairment with aging during post-exercise hyperemia. Simulation results demonstrated that the bias of IVIM-derived perfusion fraction (f p ) and diffusion of water molecules in extra-vascular tissue (D) ranged from −3.3% to 14% and from −16.5% to 0.002%, respectively, in the optimized experimental condition. The dispersion in f p and D ranged from 3.2% to 9.5% and from 0.9% to 1.1%, respectively. The mid-thigh of the left leg of four younger (21–30 year old) and four older (60–90 year old) healthy females was studied using the optimized protocol at baseline and at seven time increments occurring every 3.25 min following in-magnet dynamic knee extension exercise performed using a MR-compatible ergometer with a workload of 0.4 bar for 2.5 min. After exercise, both f p and D significantly increased in the rectus femoris (active muscle during exercise) but not in adductor magnus (inactive muscle), reflecting the fact that the local increase in perfusion with both groups showed a maximum value in the second post-exercise time-point. A significantly greater increase in perfusion from the baseline (p < 0.05) was observed in the younger group (37 ± 12.05%) compared with the older group (17.57 ± 15.92%) at the first post-exercise measurement. This work establishes a reliable non-invasive method that can be used to study the effects of aging on dynamic changes in muscle perfusion as they relate to important measures of physical function.

Article

Insights into substrate recognition and specificity for IgG by Endoglycosidase S2

by Asaminew H Aytenfisu; Daniel Deredge; Erik H Klontz; Jonathan Du; Eric Sundberg; Alexander D MacKerell

2021

Subjects
  • Health Sciences, Medicine and Surgery
  • Chemistry, Biochemistry
  • File Download
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Antibodies bind foreign antigens with high affinity and specificity leading to their neutralization and/or clearance by the immune system. The conserved N-glycan on IgG has significant impact on antibody effector function, with the endoglycosidases of Streptococcus pyogenes deglycosylating the IgG to evade the immune system, a process catalyzed by the endoglycosidase EndoS2. Studies have shown that two of the four domains of EndoS2, the carbohydrate binding module (CBM) and the glycoside hydrolase (GH) domain site are critical for catalytic activity. To yield structural insights into contributions of the CBM and the GH domains as well as the overall flexibility of EndoS2 to the proteins' catalytic activity, models of EndoS2-Fc complexes were generated through enhanced-sampling molecular-dynamics (MD) simulation and site-identification by ligand competitive saturation (SILCS) docking followed by reconstruction and multi-microsecond MD simulations. Modeling results predict that EndoS2 initially interacts with the IgG through its CBM followed by interactions with the GH yielding catalytically competent states. These may involve the CBM and GH of EndoS2 simultaneously interacting with either the same Fc CH2/CH3 domain or individually with the two Fc CH2/CH3 domains, with EndoS2 predicted to assume closed conformations in the former case and open conformations in the latter. Apo EndoS2 is predicted to sample both the open and closed states, suggesting that either complex can directly form following initial IgG-EndoS2 encounter. Interactions of the CBM and GH domains with the IgG are predicted to occur through both its glycan and protein regions. Simulations also predict that the Fc glycan can directly transfer from the CBM to the GH, facilitating formation of catalytically competent complexes and how the 734 to 751 loop on the CBM can facilitate extraction of the glycan away from the Fc CH2/CH3 domain. The predicted models are compared and consistent with Hydrogen/Deuterium Exchange data. In addition, the complex models are consistent with the high specificity of EndoS2 for the glycans on IgG supporting the validity of the predicted models.

Article

Computational Fluid Dynamics Simulations of Hemodynamics in Plaque Erosion

by Ian C. Campbell; Lucas Timmins; Don P Giddens; Renu Virmani; Alessandro Veneziani; Syed Rab; Habib Samady; Michael C McDaniel; Aloke Finn; William Taylor; John Oshinski

2013

Subjects
  • Health Sciences, Medicine and Surgery
  • Engineering, Biomedical
  • Health Sciences, Radiology
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We investigated whether local hemodynamics were associated with sites of plaque erosion and hypothesized that patients with plaque erosion have locally elevated WSS magnitude in regions where erosion has occurred. We generated 3D, patient-specific models of coronary arteries from biplane angiographic images in 3 human patients with plaque erosion diagnosed by optical coherence tomography. Using computational fluid dynamics, we simulated pulsatile blood flow and calculated both wall shear stress (WSS) and oscillatory shear index (OSI). We also investigated anatomic features of plaque erosion sites by examining branching and local curvature in X-ray angiograms of barium-perfused autopsy hearts. Neither high nor low magnitudes of mean WSS were associated with sites of plaque erosion. OSI and local curvature were also not associated with erosion. Anatomically, 8 of 13 hearts had a nearby bifurcation upstream of the site of plaque erosion. This study provides preliminary evidence that neither hemodynamics nor anatomy are predictors of plaque erosion, based upon a very unique dataset. Our sample sizes are small, but this dataset suggests that high magnitudes of WSS, one potential mechanism for inducing plaque erosion, are not necessary for erosion to occur.
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